def batch_mkcomp(tardir, outputmasterdir, mask=None):
format = "%(asctime)s: %(message)s"
logging.basicConfig(format=format, level=logging.INFO, datefmt="%H:%M:%S")
logging.info('Thread--{}--started'.format(os.path.basename(tardir)))
tarwk = re.search(r"week (\d)", tardir)
refdir = tardir.replace("week 4", "week 0", -1)
tartitle = os.path.basename(tardir)
logging.info('Thread--{}--mkdir'.format(os.path.basename(tardir)))
comptitle = tartitle[:-11] + ' w{}w{}composite'.format(0, tarwk.group(1))
outdir = os.path.join(outputmasterdir, comptitle)
if os.path.exists(outdir):
shutil.rmtree(outdir)
os.mkdir(outdir)
refimg = imreadseq(refdir,
sitkimg=False,
rmbckgrd=75,
z_range=(-300, None))
tarimg = imreadseq(tardir,
sitkimg=False,
rmbckgrd=75,
z_range=(-300, None))
composite = mkcomposite(refimg, tarimg, mask=mask)
imsaveseq(composite, outdir, comptitle, sitkimages=False)
logging.info('Thread finished for ' + comptitle)
reftitle = file.replace('week 3', 'week 0') + ' registered'
ref_img = imreadseq_multithread(os.path.join(refdir, reftitle))
tar_img = imreadseq_multithread(os.path.join(masterdir, file),
sitkimg=False,
rmbckgrd=60,
z_range=[0, 840])
tar_img = sitk.GetImageFromArray(
auto_crop(Rotate_by_Euler_angles(tar_img)))
ini_transform = cent_transform(ref_img, tar_img)
metric_values = []
multires_iterations = []
suboutput = os.path.join(masteroutput, imgtitle + " registered")
if not os.path.exists(suboutput):
os.mkdir(suboutput)
logging.info('Registration of {} is in process...'.format(imgtitle))
try:
tar_reg, tar_reg_transform = reg_transform(ref_img, tar_img,
ini_transform, imgtitle,
suboutput)
imsaveseq(tar_reg, suboutput, imgtitle + '_Reg')
logging.info('Registration of {} is finished...'.format(imgtitle))
except RuntimeError as ex:
logging.info('Registration of {} failed...'.format(imgtitle))
print(ex)
pass
logging.info("Done !")
import SimpleITK as sitk
from shubow_tools import imreadseq_multithread, imsaveseq
import os
import re
import shutil
wkdir = r"/home/blue/SITK_registered_image_14um/3rd batch tibia"
dst = r"/home/blue/SITK_registered_image_14um/Flipped"
os.chdir(wkdir)
with open("failed.txt", "r") as f:
retry_file = f.readlines()
retry_list = [i[:-1] for i in retry_file]
for fd in retry_list:
if not 'right' in fd:
continue
print(fd)
output = os.path.join(dst, fd)
if os.path.exists(output):
shutil.rmtree(output)
os.mkdir(output)
image = imreadseq_multithread(os.path.join(wkdir, fd))
image = image[::-1, :, :]
imsaveseq(image, os.path.join(dst, fd), fd)
print('Next!')